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- PDB-3ors: Crystal Structure of N5-Carboxyaminoimidazole Ribonucleotide Muta... -

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Basic information

Entry
Database: PDB / ID: 3ors
TitleCrystal Structure of N5-Carboxyaminoimidazole Ribonucleotide Mutase from Staphylococcus aureus
ComponentsN5-Carboxyaminoimidazole Ribonucleotide Mutase
KeywordsISOMERASE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBrugarolas, P. / Duguid, E.M. / Zhang, W. / Poor, C.B. / He, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus.
Authors: Brugarolas, P. / Duguid, E.M. / Zhang, W. / Poor, C.B. / He, C.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N5-Carboxyaminoimidazole Ribonucleotide Mutase
B: N5-Carboxyaminoimidazole Ribonucleotide Mutase
C: N5-Carboxyaminoimidazole Ribonucleotide Mutase
D: N5-Carboxyaminoimidazole Ribonucleotide Mutase
E: N5-Carboxyaminoimidazole Ribonucleotide Mutase
F: N5-Carboxyaminoimidazole Ribonucleotide Mutase
G: N5-Carboxyaminoimidazole Ribonucleotide Mutase
H: N5-Carboxyaminoimidazole Ribonucleotide Mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,57926
Polymers138,8498
Non-polymers1,72918
Water14,232790
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36470 Å2
ΔGint-535 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.302, 78.207, 93.039
Angle α, β, γ (deg.)90.00, 113.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N5-Carboxyaminoimidazole Ribonucleotide Mutase / Phosphoribosylaminoimidazole carboxylase catalytic subunit


Mass: 17356.186 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Gene: NWMN_0933, purE / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star
References: UniProt: A6QFS3, UniProt: A0A0H3K7Y1*PLUS, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 187255 / Num. obs: 187255 / % possible obs: 99.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 20172 / Rsym value: 0.389 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XMP

1xmp


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.139 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20255 9486 5.1 %RANDOM
Rwork0.17703 ---
obs0.17832 177862 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.85 Å2
2---0.84 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9540 0 90 790 10420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210155
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.99313801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.23851381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70426.172337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.696151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6631532
X-RAY DIFFRACTIONr_chiral_restr0.080.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217338
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.56654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.122210780
X-RAY DIFFRACTIONr_scbond_it1.91933501
X-RAY DIFFRACTIONr_scangle_it3.3164.53002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 677 -
Rwork0.24 12551 -
obs--95.7 %

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